Comment 40 for bug 331564

We cannot disable the fade plugin as this is the plugin that fades out unresponsive windows.

/apps/compiz/plugins/fade/screen0/options/window_match is set to "any & !(title=notify-osd)" so notify-OSD shouldn't be affected by this plugin anyway.

/apps/compiz/plugins/fade/screen0/options/minimize_open_close is set to true by default which seems unnecessary as these operations are performed by the animation package but toggling it does not give me any visible effect on my system. If you can reproduce the problem please try toggling this.

I have confirmed that the animation window filters are set to the correct defaults to ignore notify-osd, if you have modified them then consider resetting your compiz configuration to the defaults:
$ gconftool-2 --recursive-unset /apps/compiz